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OPENSEQ.org
DI2200006
Genes: A B A+B
Length: 71 99 163
Sequences: 260 1074 273
Seq/Len: 3.66 10.85 1.67
MirrorTree (Pazo et al. 2001) 0.85
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 1.59
2 0.00 0.00 1.58
5 0.00 0.00 1.57
10 0.00 0.00 1.57
20 0.00 0.00 1.57
100 0.00 0.00 1.58
∞ 0.00 0.00 1.61
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
59_Q 7_W 1.91 0.98 0.90
46_R 78_V 1.67 0.94 0.80
19_G 43_S 1.49 0.88 0.67
49_I 51_P 1.37 0.81 0.56
62_L 78_V 1.35 0.80 0.55
57_E 40_F 1.35 0.80 0.54
13_N 81_L 1.32 0.78 0.51
55_D 30_I 1.28 0.75 0.48
6_Q 13_S 1.27 0.74 0.47
25_S 74_E 1.26 0.73 0.46
51_A 87_K 1.26 0.73 0.45
26_L 94_K 1.25 0.72 0.44
54_Q 40_F 1.23 0.70 0.42
21_A 93_I 1.22 0.69 0.41
49_I 12_F 1.21 0.69 0.41
47_R 60_T 1.20 0.68 0.39
69_F 93_I 1.20 0.67 0.39
21_A 77_I 1.18 0.66 0.37
56_Y 40_F 1.18 0.66 0.37
30_S 35_Y 1.18 0.66 0.37
56_Y 32_S 1.17 0.64 0.36
45_Q 56_Q 1.16 0.64 0.35
18_M 81_L 1.15 0.63 0.34
56_Y 81_L 1.15 0.63 0.34
10_P 32_S 1.15 0.62 0.34
56_Y 63_R 1.12 0.60 0.31
56_Y 42_F 1.10 0.58 0.29
46_R 83_P 1.10 0.58 0.29
60_R 32_S 1.09 0.57 0.29
61_R 27_N 1.08 0.56 0.28
45_Q 7_W 1.08 0.56 0.28
50_N 80_E 1.08 0.55 0.27
11_V 20_R 1.07 0.55 0.27
46_R 66_S 1.06 0.54 0.26
10_P 64_T 1.06 0.54 0.26
19_G 44_V 1.06 0.53 0.26
15_L 26_D 1.05 0.53 0.25
19_G 92_N 1.05 0.52 0.25
11_V 30_I 1.05 0.52 0.25
55_D 7_W 1.02 0.50 0.23
61_R 64_T 1.02 0.50 0.23
36_N 13_S 1.02 0.49 0.22
17_M 72_N 1.01 0.48 0.22
23_P 92_N 1.00 0.47 0.21
62_L 88_R 0.99 0.46 0.20
44_E 65_V 0.97 0.43 0.18
12_F 45_N 0.97 0.43 0.18
23_P 90_A 0.96 0.43 0.18
52_M 77_I 0.96 0.43 0.18
41_Q 49_A 0.95 0.42 0.18
39_Q 75_I 0.95 0.42 0.17
19_G 90_A 0.95 0.42 0.17
20_K 71_D 0.93 0.40 0.16
29_P 87_K 0.93 0.39 0.16
38_Q 72_N 0.92 0.39 0.16
49_I 34_L 0.92 0.39 0.16
40_Q 55_D 0.92 0.39 0.15
44_E 59_R 0.92 0.39 0.15
51_A 30_I 0.92 0.39 0.15
38_Q 13_S 0.92 0.38 0.15
55_D 57_M 0.92 0.38 0.15
52_M 32_S 0.90 0.37 0.14
57_E 61_G 0.90 0.36 0.14
66_Q 16_S 0.90 0.36 0.14
65_E 84_Q 0.89 0.36 0.14
27_G 45_N 0.89 0.36 0.14
57_E 42_F 0.89 0.36 0.14
69_F 60_T 0.88 0.35 0.13
12_F 14_E 0.88 0.34 0.13
33_T 76_T 0.87 0.34 0.12
46_R 63_R 0.87 0.34 0.12
64_S 69_V 0.87 0.33 0.12
25_S 86_A 0.86 0.33 0.12
53_L 31_E 0.86 0.33 0.12
60_R 42_F 0.86 0.33 0.12
46_R 74_E 0.86 0.33 0.12
13_N 91_E 0.86 0.33 0.12
23_P 44_V 0.85 0.32 0.12
10_P 59_R 0.85 0.32 0.12
32_A 49_A 0.84 0.31 0.11
45_Q 90_A 0.84 0.31 0.11
19_G 20_R 0.84 0.31 0.11
50_N 62_R 0.84 0.31 0.11
11_V 32_S 0.84 0.31 0.11
66_Q 52_S 0.84 0.31 0.11
23_P 77_I 0.83 0.30 0.11
39_Q 4_T 0.83 0.30 0.10
8_E 26_D 0.83 0.30 0.10
19_G 62_R 0.83 0.30 0.10
7_P 13_S 0.83 0.30 0.10
25_S 7_W 0.82 0.30 0.10
22_S 80_E 0.82 0.29 0.10
44_E 36_S 0.82 0.29 0.10
23_P 43_S 0.81 0.29 0.10
54_Q 31_E 0.81 0.29 0.10
28_V 63_R 0.81 0.28 0.10
57_E 32_S 0.81 0.28 0.10
11_V 57_M 0.81 0.28 0.10
52_M 65_V 0.81 0.28 0.09
44_E 57_M 0.81 0.28 0.09
48_R 46_V 0.80 0.28 0.09
56_Y 31_E 0.80 0.28 0.09
60_R 35_Y 0.80 0.28 0.09
67_L 44_V 0.80 0.28 0.09
49_I 60_T 0.80 0.28 0.09
7_P 15_V 0.80 0.27 0.09
57_E 31_E 0.79 0.27 0.09
12_F 20_R 0.79 0.27 0.09
58_L 75_I 0.79 0.26 0.09
55_D 74_E 0.79 0.26 0.08
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
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